Analysis of cell velocytos with velocyto + scVelo

https://github.com/basilkhuder/Seurat-to-RNA-Velocity#generating-loom-files

Download the velocyto'd data

The problem is that velocyto is counted for individual samples. That's why we need to then also add the merged UMAPs and clusters to the merged .loom objects.

Also, from those .loom objects some of the cells did not survive the QC. That's why we need to remove them

Subset

In this part we remove the QCd cells.

Merge

Add the UMAPs and clusters from the total object

scVelo

This is the stochastic model

Get the genes that are associated with the trajectories

Calcualte pseudotime and PAGA-trajectories

Write down the model

Dynamical model

Here, we use the generalized dynamical model to solve the full transcriptional dynamics. That yields several additional insights such as latent time and identification of putative driver genes.

Cell lines as separates

K562

GDM1

RI1

Jurkat

NK-1

NK-2